Lola motif distribution in the lola peaks and the opening set genes(both at the promoter of closest gene and at the peak itself)

Compare the lola motif distribution among promoter of all genes to the that of the opening set genes and lola bound genes

Project:

Author: Vivek

Generated: Fri Mar 04 2022, 07:01 AM

## Warning in .Seqinfo.mergexy(x, y): Each of the 2 combined objects has sequence levels not in the other:
##   - in 'x': chrM, chrX_DS484099v1_random, chrX_DS484216v1_random, chrY_DS485329v1_random
##   - in 'y': chrUn_DS483562v1, chrUn_DS484160v1, chrUn_DS484280v1, chrX_DS484953v1_random
##   Make sure to always combine/compare objects based on the same reference
##   genome (use suppressWarnings() to suppress this warning).

Look at the MNase profile at Lola target genes

Lola targets are defined by Lola binding- top 1000 peaks

Project: Promoter Opening

Author: Vivek

Generated: Fri Mar 04 2022, 07:02 AM

## There are 691 positive granges and 729 negative granges
## There are 691 positive granges and 729 negative granges

## There are 691 positive granges and 729 negative granges

## There are 691 positive granges and 729 negative granges
## There are 691 positive granges and 729 negative granges

## There are 691 positive granges and 729 negative granges

## There are 364 positive granges and 372 negative granges
## There are 364 positive granges and 372 negative granges

## There are 364 positive granges and 372 negative granges

## There are 327 positive granges and 357 negative granges

## There are 327 positive granges and 357 negative granges

## There are 327 positive granges and 357 negative granges

## R version 3.6.1 (2019-07-05)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.2 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
## 
## locale:
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##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] pander_0.6.3                          scales_1.0.0                         
##  [3] matrixStats_0.55.0                    cowplot_1.0.0                        
##  [5] magrittr_1.5                          tidyr_1.0.0                          
##  [7] dplyr_0.8.3                           reshape2_1.4.3                       
##  [9] ggplot2_3.2.1                         lattice_0.20-38                      
## [11] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.52.0                      
## [13] rtracklayer_1.44.4                    Biostrings_2.52.0                    
## [15] XVector_0.24.0                        GenomicRanges_1.36.1                 
## [17] GenomeInfoDb_1.20.0                   IRanges_2.18.2                       
## [19] S4Vectors_0.22.1                      BiocGenerics_0.30.0                  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.5                  Rsamtools_2.0.0            
##  [3] assertthat_0.2.1            zeallot_0.1.0              
##  [5] digest_0.6.20               R6_2.4.0                   
##  [7] plyr_1.8.4                  backports_1.1.4            
##  [9] evaluate_0.14               pillar_1.4.2               
## [11] zlibbioc_1.30.0             rlang_0.4.0                
## [13] lazyeval_0.2.2              jquerylib_0.1.4            
## [15] Matrix_1.2-17               rmarkdown_2.11             
## [17] labeling_0.3                BiocParallel_1.18.1        
## [19] stringr_1.4.0               RCurl_1.95-4.12            
## [21] munsell_0.5.0               DelayedArray_0.10.0        
## [23] compiler_3.6.1              xfun_0.29                  
## [25] pkgconfig_2.0.2             htmltools_0.3.6            
## [27] tidyselect_0.2.5            SummarizedExperiment_1.14.1
## [29] tibble_2.1.3                GenomeInfoDbData_1.2.1     
## [31] XML_3.98-1.20               crayon_1.3.4               
## [33] withr_2.1.2                 GenomicAlignments_1.20.1   
## [35] bitops_1.0-6                grid_3.6.1                 
## [37] gtable_0.3.0                lifecycle_0.1.0            
## [39] stringi_1.4.3               ellipsis_0.2.0.1           
## [41] vctrs_0.2.0                 tools_3.6.1                
## [43] Biobase_2.44.0              glue_1.3.1                 
## [45] purrr_0.3.2                 colorspace_1.4-1           
## [47] caTools_1.17.1.2            knitr_1.24